FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2501917809> ?p ?o ?g. }

• W2501917809 abstract "Copy number variations (CNV) impact more of the cancer genome than all other mutation types combined. Recent advances in next-generation sequencing (NGS) have enabled simultaneous detection of CNVs and other somatic mutations from FFPE-derived samples, but NGS-based detection of low level CNVs (ie 2-3x) remains challenging. Nucleic acid from FFPE is a common starting material for NGS-based cancer genotyping; however, this material is often of low complexity due to a variety of factors including limited mass amount, excessive fragmentation, or chemical crosslinking. Current practices often measure input mass, or the nanograms of DNA that are added to a reaction, yet it is input complexity, or the amount of nucleic acid available for NGS library generation, that truly dictates the amount of information that can be recovered from a given sample. Archer™ VariantPlex™ assays are targeted NGS panels that permit simultaneous detection of SNVs, in/dels, and CNVs using Anchored Multiplex PCR (AMP™). Molecular barcoded adapters are ligated to each input molecule prior to any amplification. This permits the unique identification of individual input molecules thus facilitating precise copy number measurements. In addition, AMP enables amplification of highly fragmented FFPE inputs as short fragments are captured between the ligated adapter and the enrichment probe. To determine the effect of input quality on sensitivity of CNV calling we characterized over 150 tumor sample input qualities and their resulting library metrics. In addition we modeled the effect of low tumor cellularity on CNV sensitivity by carrying out dilution experiments of CNV-positive samples into samples of normal copy number. Using Archer VariantPlex assays in conjunction with Archer Analysis, we have successfully detected CNVs as small as 2X in both FFPE and cell line DNA. We found that input nucleic acid quality, as measured by a qPCR-based assay called Archer PreSeq™ DNA QC, strongly impacted the sensitivity of CNV calling. Assessment of input complexity using the PreSeq DNA QC Assay is predictive of limit of detection for CNVs and identifies an input quantity that will result in high quality NGS libraries. Our dilution experiments confirmed the expected relationship between actual and measured copy number in our population-averaging assay. Nucleic acid damage typical of FFPE samples reduces CNV calling sensitivity; however, this loss of sensitivity can be partially mitigated by increasing the input quantity. This corroborates the notion that input complexity is the major driver of information-capture from NGS based assays. Finally, tumor cellularity displays a predictable effect on the measured CNV value. Citation Format: Josh Haimes, James Covino, Namitha Namoj, Elina Baravik, Laura Johnson, Joshua Stahl, Brady P. Culver, Brian Kudlow. NGS-based CNV detection sensitivity is dependent upon nucleic acid input quality. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1381." @default.
• W2501917809 created "2016-08-23" @default.
• W2501917809 creator A5018445090 @default.
• W2501917809 creator A5022079430 @default.
• W2501917809 creator A5038212477 @default.
• W2501917809 creator A5063117437 @default.
• W2501917809 creator A5070970560 @default.
• W2501917809 creator A5073065422 @default.
• W2501917809 creator A5085406006 @default.
• W2501917809 creator A5087113586 @default.
• W2501917809 date "2016-07-15" @default.
• W2501917809 modified "2023-09-26" @default.
• W2501917809 title "Abstract 1381: NGS-based CNV detection sensitivity is dependent upon nucleic acid input quality" @default.
• W2501917809 doi "https://doi.org/10.1158/1538-7445.am2016-1381" @default.
• W2501917809 hasPublicationYear "2016" @default.
• W2501917809 type Work @default.
• W2501917809 sameAs 2501917809 @default.
• W2501917809 citedByCount "1" @default.
• W2501917809 countsByYear W25019178092019 @default.
• W2501917809 crossrefType "proceedings-article" @default.
• W2501917809 hasAuthorship W2501917809A5018445090 @default.
• W2501917809 hasAuthorship W2501917809A5022079430 @default.
• W2501917809 hasAuthorship W2501917809A5038212477 @default.
• W2501917809 hasAuthorship W2501917809A5063117437 @default.
• W2501917809 hasAuthorship W2501917809A5070970560 @default.
• W2501917809 hasAuthorship W2501917809A5073065422 @default.
• W2501917809 hasAuthorship W2501917809A5085406006 @default.
• W2501917809 hasAuthorship W2501917809A5087113586 @default.
• W2501917809 hasConcept C104317684 @default.
• W2501917809 hasConcept C111919701 @default.
• W2501917809 hasConcept C120821319 @default.
• W2501917809 hasConcept C135763542 @default.
• W2501917809 hasConcept C141231307 @default.
• W2501917809 hasConcept C177284502 @default.
• W2501917809 hasConcept C24107716 @default.
• W2501917809 hasConcept C2781188995 @default.
• W2501917809 hasConcept C31467283 @default.
• W2501917809 hasConcept C41008148 @default.
• W2501917809 hasConcept C54355233 @default.
• W2501917809 hasConcept C552990157 @default.
• W2501917809 hasConcept C70721500 @default.
• W2501917809 hasConcept C86803240 @default.
• W2501917809 hasConceptScore W2501917809C104317684 @default.
• W2501917809 hasConceptScore W2501917809C111919701 @default.
• W2501917809 hasConceptScore W2501917809C120821319 @default.
• W2501917809 hasConceptScore W2501917809C135763542 @default.
• W2501917809 hasConceptScore W2501917809C141231307 @default.
• W2501917809 hasConceptScore W2501917809C177284502 @default.
• W2501917809 hasConceptScore W2501917809C24107716 @default.
• W2501917809 hasConceptScore W2501917809C2781188995 @default.
• W2501917809 hasConceptScore W2501917809C31467283 @default.
• W2501917809 hasConceptScore W2501917809C41008148 @default.
• W2501917809 hasConceptScore W2501917809C54355233 @default.
• W2501917809 hasConceptScore W2501917809C552990157 @default.
• W2501917809 hasConceptScore W2501917809C70721500 @default.
• W2501917809 hasConceptScore W2501917809C86803240 @default.
• W2501917809 hasLocation W25019178091 @default.
• W2501917809 hasOpenAccess W2501917809 @default.
• W2501917809 hasPrimaryLocation W25019178091 @default.
• W2501917809 hasRelatedWork W1973247408 @default.
• W2501917809 hasRelatedWork W2056921347 @default.
• W2501917809 hasRelatedWork W2132251796 @default.
• W2501917809 hasRelatedWork W2160340638 @default.
• W2501917809 hasRelatedWork W2168996700 @default.
• W2501917809 hasRelatedWork W2177921758 @default.
• W2501917809 hasRelatedWork W2310233982 @default.
• W2501917809 hasRelatedWork W2487356091 @default.
• W2501917809 hasRelatedWork W2513883126 @default.
• W2501917809 hasRelatedWork W2549314712 @default.
• W2501917809 hasRelatedWork W2736021826 @default.
• W2501917809 hasRelatedWork W2741675563 @default.
• W2501917809 hasRelatedWork W2810161687 @default.
• W2501917809 hasRelatedWork W2905292156 @default.
• W2501917809 hasRelatedWork W2955987354 @default.
• W2501917809 hasRelatedWork W3084010870 @default.
• W2501917809 hasRelatedWork W3125894855 @default.
• W2501917809 hasRelatedWork W3156239097 @default.
• W2501917809 hasRelatedWork W3196621914 @default.
• W2501917809 hasRelatedWork W3202788037 @default.
• W2501917809 isParatext "false" @default.
• W2501917809 isRetracted "false" @default.
• W2501917809 magId "2501917809" @default.
• W2501917809 workType "article" @default.